Structure of PDB 8e9h Chain L Binding Site BS01

Receptor Information
>8e9h Chain L (length=625) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WLPVWLLIALPAAGATILLLAGRRSDRWGHLLGCAMSLAAFAVGTVLFAG
MLGRSGEERAVHEALFSWVPVGGLQVDFGLQLDQLSVCFVLLITGVGSLI
HIYSIGYMAEDPDRRRFFAYLNLFLAAMLLLVLADNYLGLYAGWEGVGLA
SYLLIGFWSHKPSAATAAKKAFVVNRVGDMGLAIALMIMFATIGSISFAG
VFAAAPGLSEATLSAIGLLLLLGACGKSAQVPLQSWLGDAMEGPTPVSAL
IHAATMVTAGVYLIVRSGPIFDLAPTAQTGVVIVGAVTLLFGAIIGCAKD
DIKKALAASTMSQIGYMVLAAGLGPAGYAFAIMHLLTHGFFKAGLFLGAG
SVMHAMNDEVNMRRYGGLRKVLPVTFATFGLGYLAIIGVPPLAGFFSKDG
IIEAALGAGGARGVILGGAAILGAGITAFYMTRVMLMTFFGEKRWAANSH
PHEAPAVMTWPMILLAVGSVVSGGALAIGGTLSHWLEPVVGTHEAHHAVP
VWVVTAIVLAVVAVGIAVAYRMYARQAVPEEVPEGSALTVAARRDLYGDA
FNEAVFMRGGQTLTAAMVTVDDKAVDGTAGGLAALVSRTSDALRQVQTGF
ARSYALSMLGGSALVVAAILAVQLW
Ligand information
Ligand IDXP2
InChIInChI=1S/C51H93O24P/c1-4-7-10-13-15-17-20-22-25-35(53)67-29-32(70-37(55)27-24-19-12-9-6-3)30-69-76(65,66)75-49-47(73-50-45(63)40(58)38(56)33(28-52)71-50)43(61)42(60)44(62)48(49)74-51-46(64)41(59)39(57)34(72-51)31-68-36(54)26-23-21-18-16-14-11-8-5-2/h32-34,38-52,56-64H,4-31H2,1-3H3,(H,65,66)/t32-,33-,34-,38-,39-,40+,41+,42-,43-,44+,45+,46+,47-,48+,49+,50-,51+/m1/s1
InChIKeyQGXVEMBXLAEQBM-PUGXMYIYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)O[CH]1[CH](O[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)[CH](O)[CH](O)[CH](O)[CH]1O[CH]3O[CH](COC(=O)CCCCCCCCCC)[CH](O)[CH](O)[CH]3O)OC(=O)CCCCCCC
OpenEye OEToolkits 2.0.7CCCCCCCCCCC(=O)OCC1C(C(C(C(O1)OC2C(C(C(C(C2OP(=O)(O)OCC(COC(=O)CCCCCCCCCC)OC(=O)CCCCCCC)OC3C(C(C(C(O3)CO)O)O)O)O)O)O)O)O)O
OpenEye OEToolkits 2.0.7CCCCCCCCCCC(=O)OC[C@@H]1[C@H]([C@@H]([C@@H](C(O1)O[C@H]2[C@H]([C@@H]([C@H]([C@H]([C@@H]2OP(=O)(O)OC[C@@H](COC(=O)CCCCCCCCCC)OC(=O)CCCCCCC)O[C@@H]3[C@H]([C@H](C([C@H](O3)CO)O)O)O)O)O)O)O)O)O
ACDLabs 12.01CCCCCCCCCCC(=O)OCC(OC(=O)CCCCCCC)COP(=O)(O)OC1C(OC2OC(COC(=O)CCCCCCCCCC)C(O)C(O)C2O)C(O)C(O)C(O)C1OC1OC(CO)C(O)C(O)C1O
CACTVS 3.385CCCCCCCCCCC(=O)OC[C@H](CO[P](O)(=O)O[C@H]1[C@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@H](O)[C@@H]1O[C@@H]3O[C@H](COC(=O)CCCCCCCCCC)[C@@H](O)[C@H](O)[C@@H]3O)OC(=O)CCCCCCC
FormulaC51 H93 O24 P
Name(2R)-3-{[(R)-hydroxy({(1S,2R,3R,4R,5S,6S)-3,4,5-trihydroxy-2-(alpha-D-mannopyranosyloxy)-6-[(6-O-undecanoyl-beta-D-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate
ChEMBL
DrugBank
ZINC
PDB chain8e9h Chain L Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8e9h Structure of mycobacterial respiratory complex I.
Resolution2.7 Å
Binding residue
(original residue number in PDB)
P166 S167 T170 K173 K174 N556 E557 F560 M561 G564 Q565
Binding residue
(residue number reindexed from 1)
P162 S163 T166 K169 K170 N552 E553 F556 M557 G560 Q561
Annotation score1
Enzymatic activity
Enzyme Commision number 1.6.99.5: Transferred entry: 1.6.5.11.
Gene Ontology
Molecular Function
GO:0003954 NADH dehydrogenase activity
GO:0008137 NADH dehydrogenase (ubiquinone) activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0015990 electron transport coupled proton transport
GO:0042773 ATP synthesis coupled electron transport
Cellular Component
GO:0016020 membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8e9h, PDBe:8e9h, PDBj:8e9h
PDBsum8e9h
PubMed36952383
UniProtA0QU25

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